Contacts of the helix formed by residues 154 - 175 (chain E) in PDB entry 5K58
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 154 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E THR 3.6 4.4 + - - -
153E THR* 1.3 73.6 - - - +
155E GLU* 1.3 80.9 + - - +
156E THR* 3.1 20.8 + - - -
157E LEU* 3.2 23.0 + - + +
158E LEU* 3.0 18.9 + - - +
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Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 4.4 17.0 - - + +
140E MET* 4.0 9.2 - - + +
141E ARG* 3.5 47.6 + - + +
151E TYR* 3.5 34.1 - - + +
153E THR 3.2 15.1 - - - +
154E ASP* 1.3 84.2 + - - +
156E THR* 1.3 58.0 + - - +
158E LEU* 3.4 9.7 - - - +
159E ALA* 3.0 27.4 + - - +
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Residues in contact with THR 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 4.0 4.4 - - - +
137E ARG* 3.6 42.1 - - - +
154E ASP* 3.2 13.5 + - - -
155E GLU* 1.3 75.9 - - - +
157E LEU* 1.3 51.3 + - - +
158E LEU 3.0 5.2 - - - -
159E ALA* 4.3 1.1 - - - +
160E SER* 2.7 33.6 + - - -
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Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E THR* 6.0 2.2 - - - -
154E ASP* 3.2 26.2 + - + +
156E THR* 1.3 77.8 - - - +
158E LEU* 1.3 57.7 + - - +
160E SER* 3.0 14.3 + - - -
161E GLN* 3.7 12.6 + - - +
185F ASP* 3.7 23.8 - - + +
188F ALA* 3.7 24.5 - - + -
189F ARG* 3.4 49.3 + - + +
192F LEU* 4.4 6.8 - - + +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E MET* 4.1 17.9 - - + -
151E TYR* 4.0 29.4 - - + -
153E THR* 3.2 33.0 - - - +
154E ASP 3.0 9.2 + - - +
155E GLU* 3.4 10.8 - - - +
156E THR 3.0 0.2 - - - -
157E LEU* 1.3 76.4 - - - +
159E ALA* 1.3 66.6 + - - +
160E SER 3.1 1.3 - - - -
161E GLN* 2.9 6.2 + - + +
162E ILE* 2.9 31.6 + - + +
196E GLN* 3.1 29.2 - - + +
197E LEU* 4.6 2.9 - - + -
192F LEU* 3.6 21.1 - - + -
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Residues in contact with ALA 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 3.7 32.2 - - + +
136E LEU* 3.9 15.1 - - + +
137E ARG* 4.1 10.8 - - + +
140E MET* 4.0 9.8 - - + +
155E GLU 3.0 15.1 + - - +
156E THR 3.7 3.6 + - - +
158E LEU* 1.3 78.8 - - - +
160E SER* 1.3 62.3 + - - +
162E ILE* 3.6 6.3 + - - +
163E LEU* 3.1 26.2 + - - +
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Residues in contact with SER 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLU* 4.0 18.7 + - - -
156E THR 2.7 22.6 + - - -
157E LEU* 3.0 19.1 + - - -
159E ALA* 1.3 76.6 - - - +
161E GLN* 1.3 50.0 + - - -
163E LEU* 3.2 2.4 + - - +
164E ALA* 2.5 40.5 + - - +
169F MET* 6.1 1.8 - - - -
172F ARG* 4.7 16.0 + - - +
180F TYR* 5.7 3.1 - - - -
189F ARG* 3.3 19.3 + - - -
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Residues in contact with GLN 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E LEU 3.7 8.4 - - - +
158E LEU* 2.9 13.1 + - + +
160E SER* 1.3 76.9 + - - +
162E ILE* 1.3 63.9 + - + +
164E ALA* 3.3 6.8 + - - +
165E PHE* 3.0 23.0 + - - +
196E GLN* 4.1 23.6 + - + +
165F PHE* 3.3 37.1 - - + -
189F ARG* 3.4 46.5 + - - +
192F LEU* 3.9 23.2 - - + +
193F ILE* 4.5 7.9 - - - +
196F GLN* 5.2 0.4 - - - +
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Residues in contact with ILE 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.4 14.1 - - + -
92E VAL* 3.7 28.7 - - + -
136E LEU* 3.8 15.7 - - + -
140E MET* 3.7 37.7 - - + -
158E LEU* 2.9 19.7 + - + +
159E ALA* 3.7 7.2 - - - +
161E GLN* 1.3 78.0 - - + +
163E LEU* 1.3 63.8 + - - +
165E PHE* 3.2 19.7 + - - +
166E CYS* 3.4 9.5 - - - -
193E ILE* 4.9 20.0 - - + -
196E GLN* 5.5 6.5 - - + +
197E LEU* 4.5 12.1 - - + -
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 3.6 31.6 - - + -
129E PHE* 3.4 54.5 - - + +
132E ILE* 4.1 12.8 - - + -
133E GLU* 4.1 13.7 - - + -
136E LEU* 4.4 7.4 - - + -
159E ALA 3.1 14.4 + - - +
160E SER* 4.0 2.0 - - - +
162E ILE* 1.3 77.5 - - - +
164E ALA* 1.3 66.1 + - - +
166E CYS* 3.1 22.2 + - + +
167E GLU* 3.2 18.3 + - + +
172F ARG* 4.8 10.1 - - - +
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Residues in contact with ALA 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER 2.5 22.7 + - - +
161E GLN* 3.4 10.5 - - - +
163E LEU* 1.3 74.3 - - - +
165E PHE* 1.3 63.2 + - - +
166E CYS 3.3 0.5 + - - -
167E GLU* 3.4 2.5 + - - +
168E GLY 3.5 0.2 + - - -
164F ALA 4.1 1.0 - - - +
165F PHE* 4.1 6.5 - - + -
168F GLY* 3.1 35.4 + - - +
169F MET* 3.6 34.8 - - + -
172F ARG* 4.2 8.2 - - - +
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Residues in contact with PHE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E VAL* 4.7 11.0 - - + -
96E LEU* 4.3 15.3 - - + -
161E GLN 3.0 12.1 + - - +
162E ILE* 3.2 13.0 - - + +
163E LEU 3.2 0.2 - - - -
164E ALA* 1.3 75.7 - - - +
166E CYS* 1.3 69.8 + - - +
168E GLY* 3.2 11.4 + - - -
169E MET* 3.3 33.0 + - + +
186E PHE* 5.4 4.9 - + - -
189E ARG* 4.2 22.2 - - + -
193E ILE* 4.2 25.1 - - + -
161F GLN* 3.9 30.1 - - - -
164F ALA* 3.8 26.3 - - + +
165F PHE* 4.5 15.2 - - + +
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Residues in contact with CYS 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E VAL* 4.6 13.0 - - - -
95E LEU* 4.3 12.1 - - + -
96E LEU* 3.7 31.4 - - + -
129E PHE* 6.3 0.2 - - + -
162E ILE* 3.4 17.5 - - - -
163E LEU* 3.1 29.7 + - + +
165E PHE* 1.3 77.7 - - - +
167E GLU* 1.3 57.9 + - - +
168E GLY 3.0 4.5 - - - -
169E MET* 3.0 6.4 + - - +
170E LEU* 2.9 39.1 + - + +
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Residues in contact with GLU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E THR* 5.6 1.0 - - - +
129E PHE* 3.3 36.2 - - + -
163E LEU* 3.2 13.0 + - + +
164E ALA 3.4 2.0 + - - +
166E CYS* 1.3 78.1 - - + +
168E GLY* 1.3 56.7 - - - +
170E LEU* 4.1 8.4 - - - +
171E SER* 3.3 25.1 + - - -
168F GLY* 3.8 14.8 - - - +
171F SER* 3.2 30.4 + - - -
172F ARG* 3.3 21.0 + - - +
175F ARG* 2.8 37.9 + - - -
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Residues in contact with GLY 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ALA 3.5 4.4 + - - -
165E PHE 3.2 3.0 + - - -
166E CYS 3.0 1.4 - - - -
167E GLU* 1.3 77.4 - - - +
169E MET* 1.3 63.2 + - - +
171E SER* 3.3 4.2 + - - -
172E ARG* 3.2 26.7 + - - +
164F ALA* 3.3 29.8 - - - -
167F GLU* 3.9 7.8 - - - +
168F GLY* 3.6 9.2 - - - -
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Residues in contact with MET 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 4.1 17.9 - - + -
165E PHE* 3.3 34.6 + - + +
166E CYS 3.0 6.7 + - - +
168E GLY* 1.3 74.2 - - - +
170E LEU* 1.3 58.8 + - - +
172E ARG* 3.1 8.7 + - - +
173E PHE* 2.8 29.1 + - - +
180E TYR* 4.4 26.0 - - + +
181E ARG 4.6 5.2 - - - +
182E PRO* 3.7 36.5 - - + +
184E ASP 5.4 2.0 - - - +
189E ARG* 4.1 27.1 - - - +
160F SER 5.6 0.2 - - - +
164F ALA* 4.2 15.9 - - - +
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Residues in contact with LEU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 4.5 17.9 - - + +
96E LEU* 5.0 5.6 - - + -
99E GLY* 3.9 27.1 - - - -
106E THR* 3.7 12.6 - - + +
109E LEU* 4.7 20.6 - - + -
110E THR* 3.1 27.6 - - + +
129E PHE* 4.9 17.0 - - + -
166E CYS* 2.9 28.8 + - + +
167E GLU* 4.4 7.9 - - - +
169E MET* 1.3 78.0 - - + +
171E SER* 1.3 59.1 + - - +
173E PHE* 3.6 7.0 - - + +
174E VAL* 3.4 15.2 + - - +
182E PRO* 4.8 11.4 - - + -
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Residues in contact with SER 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E THR* 4.3 9.2 - - - -
112E HIS* 4.7 8.7 - - - -
167E GLU 3.3 18.8 + - - -
168E GLY* 3.3 7.6 + - - -
169E MET 3.1 0.4 - - - -
170E LEU* 1.3 78.5 - - - +
172E ARG* 1.3 60.6 + - - +
173E PHE 3.2 0.2 - - - -
174E VAL* 3.2 3.4 + - - +
175E ARG* 2.9 36.4 + - - +
110F THR* 4.4 13.2 + - - -
167F GLU* 3.2 21.2 + - - +
171F SER* 4.7 6.5 + - - -
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Residues in contact with ARG 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLY 3.2 8.8 + - - +
169E MET* 3.1 12.4 + - - +
171E SER* 1.3 73.0 - - - +
173E PHE* 1.3 57.1 + - - +
174E VAL 3.1 1.0 + - - -
175E ARG* 3.5 26.4 - - - +
176E SER* 2.3 38.0 + - - -
180E TYR* 3.2 50.2 - - + +
129F PHE* 6.2 0.2 - - - -
130F GLU* 3.8 21.2 + - - -
133F GLU* 2.8 33.7 + - - -
160F SER* 4.2 9.6 + - - +
163F LEU* 4.2 11.8 - - - +
164F ALA* 5.6 6.3 - - - +
167F GLU* 3.0 29.6 - - - +
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Residues in contact with PHE 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E GLY* 3.0 27.1 - - - -
100E GLU* 3.5 16.6 - - - -
103E PRO* 3.7 10.1 - - + -
106E THR* 3.7 22.0 - - + -
169E MET 2.8 16.0 + - - +
170E LEU* 3.6 9.9 - - + +
172E ARG* 1.3 78.9 - - - +
174E VAL* 1.3 55.4 + - - +
176E SER* 4.2 0.7 - - - -
178E PHE* 3.0 68.7 + + + -
180E TYR 3.5 15.8 + - - +
181E ARG* 3.4 40.2 - - - -
182E PRO* 3.5 20.4 - - + -
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Residues in contact with VAL 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E THR* 3.7 14.1 - - + -
107E ARG* 3.9 39.1 + - + +
110E THR* 3.6 22.0 - - + +
112E HIS* 4.6 19.5 - - + +
170E LEU 3.4 15.7 + - - +
171E SER* 3.2 7.4 + - - +
172E ARG 3.1 0.2 - - - -
173E PHE* 1.3 74.9 - - - +
175E ARG* 1.3 56.8 + - - +
176E SER 2.6 17.7 + - - -
177E GLU* 2.6 24.5 + - - +
178E PHE* 4.3 8.7 - - + -
115F MET* 6.5 0.2 - - - -
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Residues in contact with ARG 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E HIS* 6.0 4.0 - - + +
171E SER* 2.9 27.0 + - - +
172E ARG* 3.5 32.4 - - - +
174E VAL* 1.3 75.7 - - + +
176E SER* 1.3 56.1 + - - +
177E GLU* 3.5 8.3 - - - +
109F LEU 5.7 1.3 - - - -
110F THR 5.6 6.1 - - - +
122F GLN* 3.5 29.8 + - - +
125F ILE* 5.5 0.2 - - - -
126F ASN* 2.7 69.6 + - - +
129F PHE* 3.5 38.4 - - - +
130F GLU* 4.7 5.3 + - - -
163F LEU* 4.7 1.2 - - - +
167F GLU* 3.1 36.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il